Protein Structure Hierarchy: Primary to Quaternary Organization

Introduction: Diversity and Hierarchy in Protein Structure

There are different protein structures, and these correspond directly to the kinds of functions that proteins perform. While many people assume that all proteins are essentially the same, this is not accurate. With numerous different kinds of proteins and a wide array of uses for them, it stands to reason that the structural organization of proteins will differ based on each protein's type and function (Murray et al., 2006). However, all proteins share a fundamental characteristic: they fold in three dimensions. The structure of proteins is organized in a hierarchy that begins with the primary structure and progresses through to the quaternary structure. Motifs and domains represent higher-level structures (Murray et al., 2006). The primary structure describes the polypeptide chain sequence of various amino acid residues (Van Holde & Mathews, 1996). That is generally where the similarities end. The wide variety of formations in protein structural organization comes from the many different sequences available in amino acid residues. Without those differences, all proteins would be much more similar to one another, but such similarity could also restrict their functions and prevent them from performing their intended biological roles.

All proteins are constructed from amino acids. A dipeptide forms when two amino acids link together. Oligopeptide is the term used for three to nine amino acids linked together, and polypeptide describes the linking of more than nine amino acids. Proteins are polypeptides and sometimes consist of multiple polypeptide chains linked together (Tooze, 1999). This can result in very complex proteins, such as those found in certain foods and in various biological processes within the human body. Typical proteins contain 135 to 165 amino acids (Tooze, 1999). While there are only 20 common amino acids, many additional amino acids exist but occur less frequently. These less common amino acids must still be collected and incorporated to ensure that a particular protein (Murray et al., 2006) develops properly and can function correctly.

Amino Acids and Polypeptide Formation

There is a definite structure to proteins that allows them to remain organized and perform their biological jobs. The primary structure is most important because it initiates the protein and comprises the most significant part of it. Without a sound primary structure, the protein will not be able to perform its assigned duties. This can lead to breakdowns of bodily functions and cause serious harm.

It is important to identify more than just the primary structure when understanding protein organization, because the primary structure alone is insufficient to provide everything the protein requires for proper form and function (Van Holde & Mathews, 1996). Other structures build around the primary structure, strengthening the protein and developing it further. The secondary structure is formed through backbone atoms and the hydrogen bonds that form between them. It is a regularly occurring structure within the protein and is essential for the proper creation and development of proteins (Murray et al., 2006). The backbone atoms serve as building blocks for this type of structure, bonding together through hydrogen interactions (Van Holde & Mathews, 1996). Loops, coils, or turns do occur in proteins; however, they are not considered stable parts of a secondary structure (Van Holde & Mathews, 1996). This does not mean they are not supposed to occur, only that they are insufficient to provide the needed stability of a protein's secondary structure.

There are only two types of secondary structures designed to be stable: alpha helices and beta sheets (Tooze, 1999). Without the stability provided by these secondary structures, proteins can fall apart or fail to form altogether (Tooze, 1999). This breakdown makes them less usable and less valuable. Within the human body, such protein degradation could become a serious health issue.

Secondary Structure: Stability Through Hydrogen Bonding

Alpha helices and beta sheets are located at the core of the protein, where they provide the highest level of secondary stability and receive the most protection from damage (Murray et al., 2006). By being positioned at the core, they function as both protectors and protected elements, making them vital components of proteins and increasing the likelihood that the protein will form correctly and function as intended. The coils, turns, and loops are more commonly found around the edges of the protein, not toward the core. While these provide the protein with much of what it needs to function correctly, stability is not among their valuable assets (Tooze, 1999).

After the secondary structures comes the tertiary structure, which is third in the hierarchy to provide structure and stability to a protein (Tooze, 1999). These structures describe how alpha helices, beta sheets, and random coils pack together and interact with one another throughout the polypeptide chain (Tooze, 1999). There are specific ways in which proteins must come together, and much of their organization originates from the tertiary level. To ensure that the protein forms correctly, the tertiary level organizes all of the components, allowing for stronger formation and providing the protein with both proper form and function (Tooze, 1999). In the human body, this is a vital component of proteins that require proper structure and organization to maintain correct biological function.

Next, and finally, comes the quaternary structure, which does not exist in all types of proteins. It is only observed when there is more than one polypeptide chain, making the protein complex (Tooze, 1999). There are many such complex proteins throughout the body, but some proteins are simple and require only the tertiary structure level in order to form and hold together. The organization of the chains, including the space between them and how they relate to one another, is described by the quaternary structure.

Conclusion: Structure Determines Function

Van Holde, K. E., & Mathews, C. K. (1996). Biochemistry. Benjamin/Cummings Publishing Co., Inc.